Soil microbiome has a significant impact on phytoparasitic nematodes. However, given the number of species present in soil, its role is difficult to study with traditional approaches. Advanced technologies, i.e. Next Generation Sequencing (NGS), allow the identification and quantitative determination of almost all species in a sample, enlarging our view about their rhizosphere effects. Metagenomic studies showed that microbial species may reach 10<sup>4 </sup>or more taxonomic units in a few g of soil. Comparing these numbers with the nematode bacterial antagonists known we can infer that biocontrol studies have yet a large space to explore. The activity of soil microbiome on nematodes can show suppressivity, but active species may remain undetected or unknown. To measure suppressive potential, a study was carried out with soil from a carnation crop with patchy <i>Meloidogyne </i>spp. infestations. After 4-years continuous croppings on tomato, 40% of pots showed nematode extinction, suggesting suppression or biological containment on a long time scale. In vitro NGS studies are needed to identify the role of a specific microbial component. The endophytic and nematode parasitic fungus <i>Pochonia chlamydosporia</i> showed differential expression of resistance and defensive genes in colonized tomato roots. Depending on the experimental approach, NGS studies provide a wide basis to understand the impact of soil microbiome and how phytonematode attacks may be balanced through management.